MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Network Comparison Type	Value Type	Gene	description	Rank	green	network_comparison	Filtered	red	Interaction Map

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Showing element 1027 to 1076 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence

description	Rank	green	network_comparison	red
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]	709	209.118	1.05413	220.438
ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [swissprot;acc:p22830]	3185	0.00001	1	0.00001
fetal brain protein 239 (239fb). [swissprot;acc:q15777]	2339	230.294	1.00452	229.258
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	748	233.483	1.05038	245.246
fibrillin 1 precursor. [swissprot;acc:p35555]	2844	0.00001	1	0.00001
fibrillin 2 precursor. [swissprot;acc:p35556]	2955
fibrillin 3. [refseq;acc:nm_032447]	2939
fibulin-1 precursor. [swissprot;acc:p23142]	2349	191.503	1.00441	192.348
fibulin-2 precursor. [swissprot;acc:p98095]	2245	190.448	1.00614	191.618
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	40	253	1.27273	322
fidgetin-like 1. [refseq;acc:nm_022116]	2078	213.814	1.00794	215.511
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	191	198.444	1.14179	226.582
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	186
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	1045	119.432	1.03121	115.817
fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071]	1375	211.908	1.02187	216.542
flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [swissprot;acc:p39748]	2831	0.00001	1	0.00001
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]	541	208.201	1.06703	222.156
flotillin-1. [swissprot;acc:o75955]	1289	213.22	1.02414	218.368
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	1224	231.524	1.02487	225.906
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	196	231.407	1.13745	263.215
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	619	202.139	1.05994	214.256
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	197	231.407	1.13745	263.215
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	198	231.394	1.13741	263.191
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	178	194.72	1.1652	226.887
fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	46	161.068	1.27053	204.642
fos-related antigen 2. [swissprot;acc:p15408]	44	161.046	1.2707	204.641
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787]	1828	200.115	1.01147	202.41
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114]	1825	200.086	1.0115	202.386
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116]	1823
frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331]	2745	201.514	1.00019	201.476
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467]	2561	210.18	1.00169	209.825
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	2551	210.148	1.00182	209.766
fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075]	2907	0.00001	1	0.00001
fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062]	2973
fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972]	3087
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	726	232.419	1.05196	244.495
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]	731	219.708	1.05187	208.874
fuse binding protein 3 (fragment). [sptrembl;acc:q92946]	2668	216.944	1.00107	217.176
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281]	1864	200.89	1.01086	203.071
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]	2124	222.788	1.00696	221.248
fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340]	2998	0.00001	1	0.00001
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	848	153.371	1.04184	147.211
g protein-coupled receptor 66. [refseq;acc:nm_006056]	2815	0.00001	1	0.00001
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849]	1855	215.542	1.0109	217.891
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170]	1631	215.533	1.01511	218.789
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	1582	170.844	1.01634	168.098
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	1580	170.769	1.01637	168.018
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	883	219.017	1.03917	227.596
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]	884
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	48	83.0461	1.26868	65.4586

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.